Re: [Bioc-devel] SV4Vectors installation problem
Dear All, I can confirm that the issue is fixed in the latest BioC / R versions. Thanks a lot. Yours, Marcin On Fri, Oct 16, 2015 at 7:09 AM, Michael Lawrence wrote: > On Thu, Oct 15, 2015 at 11:04 PM, Hervé Pagès > wrote: > > > Hi Michael, > > > > On 10/15/2015 10:08 AM, Michael Lawrence wrote: > > > >> Tangentially related, it seems like nchar is worth defining in > >> BiocGenerics, with a signature of "x". I saw that Biostrings uses > "type", > >> but I'm not sure why. > >> > > > > The 2 "nchar" methods that dispatch on the 'type' argument are from > > the Biostrings 1 era (> 9 years old) and were kept in the > > Biostrings/Biostrings1/ folder for legacy only (this code doesn't > > get evaluated, not even installed). That reminds me that it's probably > > time to get rid of all that stuff. > > > > But if we're just going to use the signature of 'x', > >> I can make nchar dispatch internally, so we don't need an R-level > generic. > >> Will that work? > >> > > > > If by "make nchar dispatch internally" you mean "turn nchar() into a > > primitive in R", like, say, length(), names(), dim(), dimnames(), `[`, > > etc... then works for me. > > > > > Essentially, yes. I've modified the methods package to support internal > dispatch within .Internal() calls. So no need to make it a primitive. Will > move ahead, thanks. > > > > Thanks, > > H. > > > > > > > >> Michael > >> > >> On Thu, Oct 15, 2015 at 5:19 AM, Morgan, Martin < > >> martin.mor...@roswellpark.org> wrote: > >> > >> > >>> > >>> -Original Message- > >>>> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf > Of > >>>> Marcin Cieslik > >>>> Sent: Thursday, October 15, 2015 7:46 AM > >>>> To: bioc-devel@r-project.org > >>>> Subject: [Bioc-devel] SV4Vectors installation problem > >>>> > >>>> Dear Bioconductors, > >>>> > >>>> Somewhere in August S4Vectors stopped installing correctly resulting > in > >>>> > >>> a: > >>> > >>>> > >>>> Creating a generic function for ‘nchar’ from package ‘base’ in package > >>>> ‘S4Vectors’ > >>>> > >>>> message (that cannot be suppressed) each time the package is loaded. > The > >>>> issue is not fixed by a fresh reinstall of bioconductor. The first > hint > >>>> > >>> of the > >>> > >>> you're right that this is a message and that it cannot be suppressed, > but > >>> the package still functions correctly, right? > >>> > >>> The problem was introduced by a change in R. The above is a > work-around. > >>> The permanent solution is now to use the current version of R (3.2.2) > and > >>> Bioc (3.2). The specific commit was > >>> > >>> > > >>> r106498 | mtmor...@fhcrc.org | 2015-07-16 15:10:40 -0400 (Thu, 16 Jul > >>> 2015) | 5 lines > >>> > >>> define nchar,Rle-method in .onLoad > >>> > >>> - work-around consequences of changed base::nchar signature for > >>>3.2.1 binary builds used in 3.2.0 > >>> > >>> > > >>> > >>> some related / belated discussion is at > >>> > >>> https://stat.ethz.ch/pipermail/r-devel/2015-October/071841.html > >>> > >>> Martin > >>> > >>> > >>> problem appears during installation > >>>> > >>>> http://pastebin.com/UpKdeNTH > >>>> > >>>> It appears I am not the only one affected a search reveals many > >>>> > >>> instances: > >>> > >>>> > >>>> e.g. > >>>> https://rpubs.com/Pazz/advanced_annotation > >>>> http://bioc.ism.ac.jp/packages/checkResults/3.1/bioc- > >>>> LATEST/S4Vectors/petty-install.html > >>>> http://biocluster.ucr.edu/~rkaundal/R_sep2015/Rrnaseq/RNAseq.html > >>>> > >>>> Thanks a lot for your work! If needed I can provide a Docker image > that &
Re: [Bioc-devel] SV4Vectors installation problem
On Thu, Oct 15, 2015 at 11:04 PM, Hervé Pagès wrote: > Hi Michael, > > On 10/15/2015 10:08 AM, Michael Lawrence wrote: > >> Tangentially related, it seems like nchar is worth defining in >> BiocGenerics, with a signature of "x". I saw that Biostrings uses "type", >> but I'm not sure why. >> > > The 2 "nchar" methods that dispatch on the 'type' argument are from > the Biostrings 1 era (> 9 years old) and were kept in the > Biostrings/Biostrings1/ folder for legacy only (this code doesn't > get evaluated, not even installed). That reminds me that it's probably > time to get rid of all that stuff. > > But if we're just going to use the signature of 'x', >> I can make nchar dispatch internally, so we don't need an R-level generic. >> Will that work? >> > > If by "make nchar dispatch internally" you mean "turn nchar() into a > primitive in R", like, say, length(), names(), dim(), dimnames(), `[`, > etc... then works for me. > > Essentially, yes. I've modified the methods package to support internal dispatch within .Internal() calls. So no need to make it a primitive. Will move ahead, thanks. > Thanks, > H. > > > >> Michael >> >> On Thu, Oct 15, 2015 at 5:19 AM, Morgan, Martin < >> martin.mor...@roswellpark.org> wrote: >> >> >>> >>> -Original Message- >>>> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of >>>> Marcin Cieslik >>>> Sent: Thursday, October 15, 2015 7:46 AM >>>> To: bioc-devel@r-project.org >>>> Subject: [Bioc-devel] SV4Vectors installation problem >>>> >>>> Dear Bioconductors, >>>> >>>> Somewhere in August S4Vectors stopped installing correctly resulting in >>>> >>> a: >>> >>>> >>>> Creating a generic function for ‘nchar’ from package ‘base’ in package >>>> ‘S4Vectors’ >>>> >>>> message (that cannot be suppressed) each time the package is loaded. The >>>> issue is not fixed by a fresh reinstall of bioconductor. The first hint >>>> >>> of the >>> >>> you're right that this is a message and that it cannot be suppressed, but >>> the package still functions correctly, right? >>> >>> The problem was introduced by a change in R. The above is a work-around. >>> The permanent solution is now to use the current version of R (3.2.2) and >>> Bioc (3.2). The specific commit was >>> >>> >>> r106498 | mtmor...@fhcrc.org | 2015-07-16 15:10:40 -0400 (Thu, 16 Jul >>> 2015) | 5 lines >>> >>> define nchar,Rle-method in .onLoad >>> >>> - work-around consequences of changed base::nchar signature for >>>3.2.1 binary builds used in 3.2.0 >>> >>> >>> >>> some related / belated discussion is at >>> >>> https://stat.ethz.ch/pipermail/r-devel/2015-October/071841.html >>> >>> Martin >>> >>> >>> problem appears during installation >>>> >>>> http://pastebin.com/UpKdeNTH >>>> >>>> It appears I am not the only one affected a search reveals many >>>> >>> instances: >>> >>>> >>>> e.g. >>>> https://rpubs.com/Pazz/advanced_annotation >>>> http://bioc.ism.ac.jp/packages/checkResults/3.1/bioc- >>>> LATEST/S4Vectors/petty-install.html >>>> http://biocluster.ucr.edu/~rkaundal/R_sep2015/Rrnaseq/RNAseq.html >>>> >>>> Thanks a lot for your work! If needed I can provide a Docker image that >>>> reproduces the problem. >>>> >>>> Yours, >>>> Marcin >>>> >>>>[[alternative HTML version deleted]] >>>> >>>> ___ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >>> >>> >>> This email message may contain legally privileged and/or confidential >>> information. If you are not the intended recipient(s), or the employee >>> or >>> agent responsible for the delivery of this message to the intended >>> recipient(s), you are hereby notified that any disclosure, copying, >>> distribution, or use of this email message is prohibited. If you have >>> received this message in error, please notify the sender immediately by >>> e-mail and delete this email message from your computer. Thank you. >>> ___ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> >> [[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax:(206) 667-1319 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] SV4Vectors installation problem
Hi Michael, On 10/15/2015 10:08 AM, Michael Lawrence wrote: Tangentially related, it seems like nchar is worth defining in BiocGenerics, with a signature of "x". I saw that Biostrings uses "type", but I'm not sure why. The 2 "nchar" methods that dispatch on the 'type' argument are from the Biostrings 1 era (> 9 years old) and were kept in the Biostrings/Biostrings1/ folder for legacy only (this code doesn't get evaluated, not even installed). That reminds me that it's probably time to get rid of all that stuff. But if we're just going to use the signature of 'x', I can make nchar dispatch internally, so we don't need an R-level generic. Will that work? If by "make nchar dispatch internally" you mean "turn nchar() into a primitive in R", like, say, length(), names(), dim(), dimnames(), `[`, etc... then works for me. Thanks, H. Michael On Thu, Oct 15, 2015 at 5:19 AM, Morgan, Martin < martin.mor...@roswellpark.org> wrote: -Original Message- From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of Marcin Cieslik Sent: Thursday, October 15, 2015 7:46 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] SV4Vectors installation problem Dear Bioconductors, Somewhere in August S4Vectors stopped installing correctly resulting in a: Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ message (that cannot be suppressed) each time the package is loaded. The issue is not fixed by a fresh reinstall of bioconductor. The first hint of the you're right that this is a message and that it cannot be suppressed, but the package still functions correctly, right? The problem was introduced by a change in R. The above is a work-around. The permanent solution is now to use the current version of R (3.2.2) and Bioc (3.2). The specific commit was r106498 | mtmor...@fhcrc.org | 2015-07-16 15:10:40 -0400 (Thu, 16 Jul 2015) | 5 lines define nchar,Rle-method in .onLoad - work-around consequences of changed base::nchar signature for 3.2.1 binary builds used in 3.2.0 some related / belated discussion is at https://stat.ethz.ch/pipermail/r-devel/2015-October/071841.html Martin problem appears during installation http://pastebin.com/UpKdeNTH It appears I am not the only one affected a search reveals many instances: e.g. https://rpubs.com/Pazz/advanced_annotation http://bioc.ism.ac.jp/packages/checkResults/3.1/bioc- LATEST/S4Vectors/petty-install.html http://biocluster.ucr.edu/~rkaundal/R_sep2015/Rrnaseq/RNAseq.html Thanks a lot for your work! If needed I can provide a Docker image that reproduces the problem. Yours, Marcin [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] SV4Vectors installation problem
Tangentially related, it seems like nchar is worth defining in BiocGenerics, with a signature of "x". I saw that Biostrings uses "type", but I'm not sure why. But if we're just going to use the signature of 'x', I can make nchar dispatch internally, so we don't need an R-level generic. Will that work? Michael On Thu, Oct 15, 2015 at 5:19 AM, Morgan, Martin < martin.mor...@roswellpark.org> wrote: > > > > -Original Message- > > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > > Marcin Cieslik > > Sent: Thursday, October 15, 2015 7:46 AM > > To: bioc-devel@r-project.org > > Subject: [Bioc-devel] SV4Vectors installation problem > > > > Dear Bioconductors, > > > > Somewhere in August S4Vectors stopped installing correctly resulting in > a: > > > > Creating a generic function for ‘nchar’ from package ‘base’ in package > > ‘S4Vectors’ > > > > message (that cannot be suppressed) each time the package is loaded. The > > issue is not fixed by a fresh reinstall of bioconductor. The first hint > of the > > you're right that this is a message and that it cannot be suppressed, but > the package still functions correctly, right? > > The problem was introduced by a change in R. The above is a work-around. > The permanent solution is now to use the current version of R (3.2.2) and > Bioc (3.2). The specific commit was > > > r106498 | mtmor...@fhcrc.org | 2015-07-16 15:10:40 -0400 (Thu, 16 Jul > 2015) | 5 lines > > define nchar,Rle-method in .onLoad > > - work-around consequences of changed base::nchar signature for > 3.2.1 binary builds used in 3.2.0 > > > > some related / belated discussion is at > > https://stat.ethz.ch/pipermail/r-devel/2015-October/071841.html > > Martin > > > > problem appears during installation > > > > http://pastebin.com/UpKdeNTH > > > > It appears I am not the only one affected a search reveals many > instances: > > > > e.g. > > https://rpubs.com/Pazz/advanced_annotation > > http://bioc.ism.ac.jp/packages/checkResults/3.1/bioc- > > LATEST/S4Vectors/petty-install.html > > http://biocluster.ucr.edu/~rkaundal/R_sep2015/Rrnaseq/RNAseq.html > > > > Thanks a lot for your work! If needed I can provide a Docker image that > > reproduces the problem. > > > > Yours, > > Marcin > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] SV4Vectors installation problem
> -Original Message- > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > Marcin Cieslik > Sent: Thursday, October 15, 2015 7:46 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] SV4Vectors installation problem > > Dear Bioconductors, > > Somewhere in August S4Vectors stopped installing correctly resulting in a: > > Creating a generic function for ‘nchar’ from package ‘base’ in package > ‘S4Vectors’ > > message (that cannot be suppressed) each time the package is loaded. The > issue is not fixed by a fresh reinstall of bioconductor. The first hint of the you're right that this is a message and that it cannot be suppressed, but the package still functions correctly, right? The problem was introduced by a change in R. The above is a work-around. The permanent solution is now to use the current version of R (3.2.2) and Bioc (3.2). The specific commit was r106498 | mtmor...@fhcrc.org | 2015-07-16 15:10:40 -0400 (Thu, 16 Jul 2015) | 5 lines define nchar,Rle-method in .onLoad - work-around consequences of changed base::nchar signature for 3.2.1 binary builds used in 3.2.0 some related / belated discussion is at https://stat.ethz.ch/pipermail/r-devel/2015-October/071841.html Martin > problem appears during installation > > http://pastebin.com/UpKdeNTH > > It appears I am not the only one affected a search reveals many instances: > > e.g. > https://rpubs.com/Pazz/advanced_annotation > http://bioc.ism.ac.jp/packages/checkResults/3.1/bioc- > LATEST/S4Vectors/petty-install.html > http://biocluster.ucr.edu/~rkaundal/R_sep2015/Rrnaseq/RNAseq.html > > Thanks a lot for your work! If needed I can provide a Docker image that > reproduces the problem. > > Yours, > Marcin > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] SV4Vectors installation problem
Dear Bioconductors, Somewhere in August S4Vectors stopped installing correctly resulting in a: Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ message (that cannot be suppressed) each time the package is loaded. The issue is not fixed by a fresh reinstall of bioconductor. The first hint of the problem appears during installation http://pastebin.com/UpKdeNTH It appears I am not the only one affected a search reveals many instances: e.g. https://rpubs.com/Pazz/advanced_annotation http://bioc.ism.ac.jp/packages/checkResults/3.1/bioc-LATEST/S4Vectors/petty-install.html http://biocluster.ucr.edu/~rkaundal/R_sep2015/Rrnaseq/RNAseq.html Thanks a lot for your work! If needed I can provide a Docker image that reproduces the problem. Yours, Marcin [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
